Biomedical Engineering Reference
In-Depth Information
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delivering tailored biomarker discovery solutions to identify and
validate the best biomarkers for all diagnostic applications;
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licensing fundamental microarrays and other patents;
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developing new diagnostic techniques with potential for in-house
commercialisation or partnering with diagnostic and pharmaceutical
organisations;
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delivering a comprehensive sequencing service using next-generation
sequencing technologies.
Here, I will describe the approach that OGT has taken in the development
of our in-house, 'omics platform. This covers the initial stages of setting
up a commercial platform to service customer microarrays, through to
developing our own microarray products, running high-throughput
projects to recently setting up a pipeline to assemble and annotate data
from next-generation sequencers. Each of these has required a range of
software applications. Whenever OGT requires new software, a standard
approach of evaluating all possible options is followed, be they FLOSS,
commercial or even commissioned; weighing up the advantages and
disadvantages of each solution. Obviously an important consideration is
cost, and where there are comparable products then this becomes an
important part of any discussion to decide which products to use.
However, cost is just one of a series of important factors such as ease of
use, quality of output and the presence/absence of specifi c skills within
the group. Furthermore, any likely impact on infrastructure must also be
borne in mind before a decision is made. In reality, more often than not a
FLOSS alternative will be selected, indicating just how much high-quality
FLOSS software is now available.
10.2 General changes over time
The computational biology group at OGT has evolved hugely over this
time. In 2003, OGT was a small biotechnology company with a staff
numbering in the low 20s, servicing mostly small academic projects for
customers within the UK. Since then, the company has grown to more
than 70 full-time employees and has customers from both industry and
academia based around the globe. Concomitantly, the typical value of
projects has greatly increased from the low thousands of pounds involving
a handful of arrays, to hundreds of thousands based on thousands of
microarrays. To cope with this growth, our internal procedures and
processes have had to develop and evolve.
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